A C D G O R S T U X

A

add(String, String, String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

Adds information to the log file.

addOtherNameLog(String, String, String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.DescriptionLineRules

Not implemented

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.GrammarRules

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.OrderedRules

Applies the rules.

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.ReactionRules

Applies the rules.

applyRules(String) - Method in interface uk.ac.ebi.intenz.tools.sib.translator.rules.RuleGroup

Implementations of this interface must implement this method to translate text based on rules.

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.TagRules

Applies the rules.

applyRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.UnorderedRules

Applies the rules.

C

close() - Method in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

Must be called to close the log file.

COMMENTS - Static variable in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

COMMON_NAMES - Static variable in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

D

DescriptionLineRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

DescriptionLineRules are specific to the description line.

G

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.DescriptionLineRules

Returns the sole instance of this class.

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.GrammarRules

Returns the sole instance of this class.

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.OrderedRules

Returns the sole instance of this class.

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.ReactionRules

Returns the sole instance of this class.

getInstance(SpecialCharacters) - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.TagRules

Returns the sole instance of this class.

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.rules.UnorderedRules

Returns the sole instance of this class.

getInstance() - Static method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Returns the sole instance of this class.

GrammarRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

GrammarRules

O

OrderedRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

This singleton class stores regular expression rules to be used to transform text.

OTHER_NAMES - Static variable in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

R

ReactionRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

This singleton class stores regular expression rules to be used to transform text.

REACTIONS - Static variable in class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.DescriptionLineRules

Applies the reverse rules.

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.GrammarRules

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.OrderedRules

Applies the reverse rules.

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.ReactionRules

Applies the reverse rules.

reverseRules(String) - Method in interface uk.ac.ebi.intenz.tools.sib.translator.rules.RuleGroup

This method can be used to reverse the rules which have been applied in RuleGroup.applyRules(String).

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.TagRules

Calls TagRules.applyRules(String) only.

reverseRules(String) - Method in class uk.ac.ebi.intenz.tools.sib.translator.rules.UnorderedRules

Applies the reverse rules.

RuleGroup - Interface in uk.ac.ebi.intenz.tools.sib.translator.rules

This interface defines the mandatory method for all RuleGroup implementations.

S

SIBEnzymeLogger - Class in uk.ac.ebi.intenz.tools.sib.translator

This class is used to log translation activities during the parse process.

SIBEnzymeLogger(String, String) - Constructor for class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

Initialises the log file of the given EC.

SIBEnzymeLogger(String, int, boolean) - Constructor for class uk.ac.ebi.intenz.tools.sib.translator.SIBEnzymeLogger

Enables a logger which stores all results in one file.

T

TagRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

This singleton class stores regular expression rules to be used to transform text.

toASCII(String, boolean) - Method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Deprecated.

Use toAscii(String text, boolean useReactionRules, boolean useDeLineRules)

toASCII(String, boolean, boolean) - Method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Translates a XChars encoded string into its ASCII representation.

toASCII(String, boolean, boolean, boolean) - Method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Translates a XChars encoded string into its ASCII representation.

toXCharsFormat(String, boolean) - Method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Translates a string into the IntEnz format.

toXCharsFormat(List, boolean) - Method in class uk.ac.ebi.intenz.tools.sib.translator.XCharsASCIITranslator

Just calls XCharsASCIITranslator.toXCharsFormat(String, boolean) method for each item.

U

uk.ac.ebi.intenz.tools.sib.translator - package uk.ac.ebi.intenz.tools.sib.translator

These classes are used to transfer ENZYME data into the IntEnz format and vice versa.

uk.ac.ebi.intenz.tools.sib.translator.rules - package uk.ac.ebi.intenz.tools.sib.translator.rules

This package consists of the rule classes used by the translator.

UnorderedRules - Class in uk.ac.ebi.intenz.tools.sib.translator.rules

This singleton class stores regular expression rules to be used to transform text.

X

XCharsASCIITranslator - Class in uk.ac.ebi.intenz.tools.sib.translator

This class translates ENZYME data into the IntEnz format and vice versa.

A C D G O R S T U X